[[Matzke|Nick]] is working on developing a Biogeography module for BioPython. This work is funded by [http://socghop.appspot.com/program/home/google/gsoc2009 Google Summer of Code 2009] through NESCENT's [https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009 Phyloinformatics Summer of Code 2009]. See the project proposal at: [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798250 Biogeographical Phylogenetics for BioPython]. The mentors are [http://blackrim.org/ Stephen Smith] (primary), [http://bcbio.wordpress.com/ Brad Chapman], and [http://evoviz.nescent.org/ David Kidd]. The code currently lives at the [http://github.com/nmatzke/biopython/tree/Geography Geography fork of the nmatzke branch on GitHub], and you can see a timeline and other info about ongoing development [[BioGeography|here]]. The new module is being documented on this wiki as [[BioGeography]].

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[[Matzke|Nick]] is working on developing a Biogeography module for BioPython. This work is funded by [http://socghop.appspot.com/program/home/google/gsoc2009 Google Summer of Code 2009] through NESCENT's [https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009 Phyloinformatics Summer of Code 2009]. See the project proposal at: [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798250 Biogeographical Phylogenetics for BioPython]. The mentors are [http://blackrim.org/ Stephen Smith] (primary), [http://bcbio.wordpress.com/ Brad Chapman], and [http://evoviz.nescent.org/ David Kidd]. The code currently lives at the Bio/Geography directory of the [http://github.com/nmatzke/biopython/tree/Geography Geography fork of the nmatzke branch on GitHub], and you can see a timeline and other info about ongoing development [[BioGeography|here]]. The new module is being documented on this wiki as [[BioGeography]].

=== Roche 454 SFF parsing in Bio.SeqIO ===

=== Roche 454 SFF parsing in Bio.SeqIO ===

Revision as of 21:51, 22 May 2009

This page provides a central location to collect references to active projects. This is a good place to start if you are interested in contributing to Biopython and want to find larger projects in progress. For developers, use this to reference git branches or other projects which you will be working on for an extended period of time. Please keep it up to date as projects are finished and integrated into Biopython.

GFF parser

PhyloXML driver (GSoC)

Eric is working on supporting the PhyloXML format, as a project for Google Summer of Code 2009. Brad is mentoring this project. The code lives on a branch in GitHub, and you can see a timeline and other info about ongoing development here. The new module is being documented on this wiki as PhyloXML.

Roche 454 SFF parsing in Bio.SeqIO

Open Enhancement Bugs

This Bugzilla Search will list all open enhancement bugs (any filed by core developers are fairly likely to be integrated, some are just wish list entries).

Project ideas

Please add any ideas or proposals for new additions to Biopython. Bugs and enhancements for current code should be discussed though our bugzilla interface.

Use SQLAlchemy, an object relational mapper, for BioSQL internals. This would add an additional external dependency to Biopython, but provides ready support for additional databases like SQLite. It also would provide a raw object interface to BioSQL databases when the SeqRecord-like interface is not sufficient. Brad has some initial code for this.

Enhancement list

Maintaining software involves incremental improvements for new format changes and removal of bugs. Please see our bugzilla page for a current list. Post to the developer mailing list if you are interested in tackling any open issues.